1
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Alberti M, Sainas S, Ronchi E, Lolli ML, Boschi D, Rizzi M, Ferraris DM, Miggiano R. Biochemical characterization of Mycobacterium tuberculosis dihydroorotate dehydrogenase and identification of a selective inhibitor. FEBS Lett 2023; 597:2119-2132. [PMID: 37278160 DOI: 10.1002/1873-3468.14680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 05/24/2023] [Accepted: 05/25/2023] [Indexed: 06/07/2023]
Abstract
Mycobacterium tuberculosis (MTB) is the etiologic agent of tuberculosis (TB), an ancient disease which causes 1.5 million deaths worldwide. Dihydroorotate dehydrogenase (DHODH) is a key enzyme of the MTB de novo pyrimidine biosynthesis pathway, and it is essential for MTB growth in vitro, hence representing a promising drug target. We present: (i) the biochemical characterization of the full-length MTB DHODH, including the analysis of the kinetic parameters, and (ii) the previously unreleased crystal structure of the protein that allowed us to rationally screen our in-house chemical library and identify the first selective inhibitor of mycobacterial DHODH. The inhibitor has fluorescence properties, potentially instrumental to in cellulo imaging studies, and exhibits an IC50 value of 43 μm, paving the way to hit-to-lead process.
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Affiliation(s)
- Marta Alberti
- Department of Pharmaceutical Sciences, University of Eastern Piedmont, Novara, Italy
| | - Stefano Sainas
- Department of Sciences and Drug Technology, University of Turin, Torino, Italy
| | - Erika Ronchi
- Department of Pharmaceutical Sciences, University of Eastern Piedmont, Novara, Italy
| | - Marco L Lolli
- Department of Sciences and Drug Technology, University of Turin, Torino, Italy
| | - Donatella Boschi
- Department of Sciences and Drug Technology, University of Turin, Torino, Italy
| | - Menico Rizzi
- Department of Pharmaceutical Sciences, University of Eastern Piedmont, Novara, Italy
| | - Davide M Ferraris
- Department of Pharmaceutical Sciences, University of Eastern Piedmont, Novara, Italy
| | - Riccardo Miggiano
- Department of Pharmaceutical Sciences, University of Eastern Piedmont, Novara, Italy
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2
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Hidayati AR, Melinda, Ilmi H, Sakura T, Sakaguchi M, Ohmori J, Hartuti ED, Tumewu L, Inaoka DK, Tanjung M, Yoshida E, Tokumasu F, Kita K, Mori M, Dobashi K, Nozaki T, Syafruddin D, Hafid AF, Waluyo D, Widyawaruyanti A. Effect of geranylated dihydrochalcone from Artocarpus altilis leaves extract on Plasmodium falciparum ultrastructural changes and mitochondrial malate: Quinone oxidoreductase. Int J Parasitol Drugs Drug Resist 2022; 21:40-50. [PMID: 36565667 PMCID: PMC9798170 DOI: 10.1016/j.ijpddr.2022.12.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 12/05/2022] [Accepted: 12/06/2022] [Indexed: 12/13/2022]
Abstract
Nearly half of the world's population is at risk of being infected by Plasmodium falciparum, the pathogen of malaria. Increasing resistance to common antimalarial drugs has encouraged investigations to find compounds with different scaffolds. Extracts of Artocarpus altilis leaves have previously been reported to exhibit in vitro antimalarial activity against P. falciparum and in vivo activity against P. berghei. Despite these initial promising results, the active compound from A. altilis is yet to be identified. Here, we have identified 2-geranyl-2', 4', 3, 4-tetrahydroxy-dihydrochalcone (1) from A. altilis leaves as the active constituent of its antimalarial activity. Since natural chalcones have been reported to inhibit food vacuole and mitochondrial electron transport chain (ETC), the morphological changes in food vacuole and biochemical inhibition of ETC enzymes of (1) were investigated. In the presence of (1), intraerythrocytic asexual development was impaired, and according to the TEM analysis, this clearly affected the ultrastructure of food vacuoles. Amongst the ETC enzymes, (1) inhibited the mitochondrial malate: quinone oxidoreductase (PfMQO), and no inhibition could be observed on dihydroorotate dehydrogenase (DHODH) as well as bc1 complex activities. Our study suggests that (1) has a dual mechanism of action affecting the food vacuole and inhibition of PfMQO-related pathways in mitochondria.
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Affiliation(s)
- Agriana Rosmalina Hidayati
- Doctoral Program, Faculty of Pharmacy, Universitas Airlangga, Surabaya, Indonesia,Department of Pharmacy, Faculty of Medicine, Universitas Mataram, Mataram, Indonesia
| | - Melinda
- Research Center for Genetic Engineering, National Research and Innovation Agency (BRIN), Bogor, Indonesia
| | - Hilkatul Ilmi
- Center of Natural Product Medicine Research and Development, Institute of Tropical Disease, Universitas Airlangga, Surabaya, Indonesia
| | - Takaya Sakura
- Department of Molecular Infection Dynamics, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki, Japan,School of Tropical Medicine and Global Health, Nagasaki University, Nagasaki, Japan
| | - Miako Sakaguchi
- Central Laboratory, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki, Japan
| | - Junko Ohmori
- School of Tropical Medicine and Global Health, Nagasaki University, Nagasaki, Japan
| | - Endah Dwi Hartuti
- Research Center for Genetic Engineering, National Research and Innovation Agency (BRIN), Bogor, Indonesia,Graduate School of Biomedical Science, Nagasaki University, Nagasaki, Japan
| | - Lidya Tumewu
- Center of Natural Product Medicine Research and Development, Institute of Tropical Disease, Universitas Airlangga, Surabaya, Indonesia
| | - Daniel Ken Inaoka
- Department of Molecular Infection Dynamics, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki, Japan,School of Tropical Medicine and Global Health, Nagasaki University, Nagasaki, Japan,Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Japan
| | - Mulyadi Tanjung
- Department of Chemistry, Faculty of Science and Technology, Universitas Airlangga, Surabaya, Indonesia
| | - Eri Yoshida
- Department of Molecular Infection Dynamics, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki, Japan
| | - Fuyuki Tokumasu
- Department of Cellular Architecture Studies, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki, Japan
| | - Kiyoshi Kita
- School of Tropical Medicine and Global Health, Nagasaki University, Nagasaki, Japan,Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Japan,Department of Host-Defense Biochemistry, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki, Japan
| | - Mihoko Mori
- Kitasato Institute for Life Science, Kitasato University, Tokyo, Japan
| | - Kazuyuki Dobashi
- Kitasato Institute for Life Science, Kitasato University, Tokyo, Japan
| | - Tomoyoshi Nozaki
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Japan
| | - Din Syafruddin
- Department of Parasitology, Faculty of Medicine, Hasanudin University, Makassar, Indonesia
| | - Achmad Fuad Hafid
- Center of Natural Product Medicine Research and Development, Institute of Tropical Disease, Universitas Airlangga, Surabaya, Indonesia,Department of Pharmaceutical Sciences, Faculty of Pharmacy, Universitas Airlangga, Surabaya, Indonesia
| | - Danang Waluyo
- Research Center for Genetic Engineering, National Research and Innovation Agency (BRIN), Bogor, Indonesia
| | - Aty Widyawaruyanti
- Center of Natural Product Medicine Research and Development, Institute of Tropical Disease, Universitas Airlangga, Surabaya, Indonesia,Department of Pharmaceutical Sciences, Faculty of Pharmacy, Universitas Airlangga, Surabaya, Indonesia,Corresponding author. Center of Natural Product Medicine Research and Development, Institute of Tropical Disease, Universitas Airlangga, Surabaya, Indonesia.
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3
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Singh Y, Sharma R, Mishra M, Verma PK, Saxena AK. Crystal structure of ArOYE6 reveals a novel C‐terminal helical extension and mechanistic insights into the distinct class III OYEs from pathogenic fungi. FEBS J 2022; 289:5531-5550. [DOI: 10.1111/febs.16445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 03/02/2022] [Accepted: 03/18/2022] [Indexed: 11/28/2022]
Affiliation(s)
- Yeshveer Singh
- Plant Immunity Laboratory National Institute of Plant Genome Research New Delhi India
| | - Ruby Sharma
- Rm‐403/440 Structural Biology Laboratory School of Life Science Jawaharlal Nehru University New Delhi India
| | - Manasi Mishra
- Plant Immunity Laboratory National Institute of Plant Genome Research New Delhi India
| | - Praveen Kumar Verma
- Plant Immunity Laboratory National Institute of Plant Genome Research New Delhi India
- Plant Immunity Laboratory School of Life Science Jawaharlal Nehru University New Delhi India
| | - Ajay Kumar Saxena
- Rm‐403/440 Structural Biology Laboratory School of Life Science Jawaharlal Nehru University New Delhi India
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4
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Examination of multiple Trypanosoma cruzi targets in a new drug discovery approach for Chagas disease. Bioorg Med Chem 2022; 58:116577. [DOI: 10.1016/j.bmc.2021.116577] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 12/10/2021] [Accepted: 12/10/2021] [Indexed: 12/21/2022]
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Reis IMA, Umehara E, Conceição RS, de M Oliveira L, Dos S Junior MC, Costa-Silva TA, Amaral M, Tempone AG, Branco A, Lago JHG. γ-Lactones from Persea americana and Persea fulva - in Vitro and in Silico Evaluation of Trypanosoma cruzi Activity. Chem Biodivers 2021; 18:e2100362. [PMID: 34254435 DOI: 10.1002/cbdv.202100362] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 07/12/2021] [Indexed: 11/10/2022]
Abstract
In the present study, five known γ-lactones (majoranolide B - 1, majorenolide - 2, majorynolide - 3, lincomolide D - 4, and isolinderanolide E - 5), as well as a new one (perseanolide - 6), were isolated from Persea fulva and P. americana. All isolated compounds exhibited potential activity against trypomastigote forms of Trypanosoma cruzi, whereas compounds 2 (EC50 of 4.8 μM) and 6 (EC50 of 3.6 μM) displayed superior activity than the positive control benznidazole (EC50 of 16.4 μM), with selectivity index (SI) values of 17.8 and >55.6, respectively (benznidazole, SI>12.2). Molecular docking studies were performed for 1-6 against six T. cruzi molecular targets. Using this approach, we observed that, even though perseanolide (6) showed favorable docking to several studied targets, the results were especially promising for hypoxanthine phosphoribosyl transferase (PDB 1TC1). As PDB 1TC1 is associated to the transference of a monophosphorylated ribose from phosphoribosylpyrophosphate (PRPP) in the ribonucleotide synthesis pathway, this interaction may affect the survival of T. cruzi in mammalian cells. The data herein also indicate that possible intermolecular interactions between 6 and PDB 1TC1 derive from (i) hydrogen bonds in the α,β-unsaturated-γ-lactone unity and (ii) hydrophobic interactions in the long-chain alkyl group. Based on our results, perseanolide (6), reported for the first time in this work, can auspiciously contribute to future works regarding new trypanocidal agents.
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Affiliation(s)
- Isabella Mary A Reis
- Departamento de Saúde, Universidade Estadual de Feira de Santana, 44036-900, Feira de Santana, BA, Brazil
| | - Eric Umehara
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, 09210-580, Santo Andre, SP, Brazil
| | - Rodrigo S Conceição
- Departamento de Saúde, Universidade Estadual de Feira de Santana, 44036-900, Feira de Santana, BA, Brazil
| | - Larissa de M Oliveira
- Departamento de Saúde, Universidade Estadual de Feira de Santana, 44036-900, Feira de Santana, BA, Brazil
| | | | - Thais A Costa-Silva
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, 09210-580, Santo Andre, SP, Brazil
| | - Maiara Amaral
- Centro de Parasitologia e Micologia, Instituto Adolfo Lutz, 01246-902, São Paulo, SP, Brazil
| | - Andre G Tempone
- Centro de Parasitologia e Micologia, Instituto Adolfo Lutz, 01246-902, São Paulo, SP, Brazil
| | - Alexsandro Branco
- Departamento de Saúde, Universidade Estadual de Feira de Santana, 44036-900, Feira de Santana, BA, Brazil
| | - João Henrique G Lago
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, 09210-580, Santo Andre, SP, Brazil
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6
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Yasuo N, Ishida T, Sekijima M. Computer aided drug discovery review for infectious diseases with case study of anti-Chagas project. Parasitol Int 2021; 83:102366. [PMID: 33915269 DOI: 10.1016/j.parint.2021.102366] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 03/23/2021] [Accepted: 04/07/2021] [Indexed: 01/09/2023]
Abstract
Neglected tropical diseases (NTDs) are parasitic and bacterial infections that are widespread, especially in the tropics, and cause health problems for about one billion people over 149 countries worldwide. However, in terms of therapeutic agents, for example, nifurtimox and benznidazole were developed in the 1960s to treat Chagas disease, but new drugs are desirable because of their side effects. Drug discovery takes 12 to 14 years and costs $2.6 billon dollars, and hence, computer aided drug discovery (CADD) technology is expected to reduce the time and cost. This paper describes our methods and results based on CADD, mainly for NTDs. An overview of databases, molecular simulation and pharmacophore modeling, contest-based drug discovery, and machine learning and their results are presented herein.
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Affiliation(s)
- Nobuaki Yasuo
- Academy for Convergence of Materials and Informatics (TAC-MI), Tokyo Institute of Technology, S6-23, 2-12-1, Ookayama, Meguro-ku, Tokyo, Japan.
| | - Takashi Ishida
- Department of Computer Science, School of Computing, Tokyo Institute of Technology, W8-85, 2-12-1, Ookayama, Meguro-ku, Tokyo, Japan.
| | - Masakazu Sekijima
- Department of Computer Science, School of Computing, Tokyo Institute of Technology, 4259-J3-23, Nagatsuta-cho, Midori-ku, Yokohama, 226-8501, Japan.
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7
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Bombaça ACS, Silva LA, Chaves OA, da Silva LS, Barbosa JMC, da Silva AM, Ferreira ABB, Menna-Barreto RFS. Novel N,N-di-alkylnaphthoimidazolium derivative of β-lapachone impaired Trypanosoma cruzi mitochondrial electron transport system. Biomed Pharmacother 2021; 135:111186. [PMID: 33395606 DOI: 10.1016/j.biopha.2020.111186] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 12/16/2020] [Accepted: 12/26/2020] [Indexed: 11/19/2022] Open
Abstract
Trypanosoma cruzi is a protozoan parasite that causes Chagas disease, a neglected tropical disease that is endemic in Latin America and spreading worldwide due to globalization. The current treatments are based on benznidazole and nifurtimox; however, these drugs have important limitations and limited efficacy during the chronic phase, reinforcing the necessity of an alternative chemotherapy. For the last 30 years, our group has been evaluating the biological activity of naphthoquinones and derivatives on T. cruzi, and of the compounds tested, N1, N2 and N3 were found to be the most active in vitro. Here, we show the synthesis of a novel β-lapachone-derived naphthoimidazolium named N4 and assess its activity on T. cruzi stages and the mechanism of action. The new compound was very active on all parasite stages (IC50/24 h in the range of 0.8-7.9 μM) and had a selectivity index of 5.4. Mechanistic analyses reveal that mitochondrial ROS production begins after short treatment starts and primarily affects the activity of complexes II-III. After 24 h treatment, a partial restoration of mitochondrial physiology (normal complexes II-III and IV activities and controlled H2O2 release) was observed; however, an extensive injury in its morphology was still detected. During treatment with N4, we also observed that trypanothione reductase activity increased in a time-dependent manner and concomitant with increased oxidative stress. Molecular docking calculations indicated the ubiquinone binding site of succinate dehydrogenase as an important interaction point with N4, as with the FMN binding site of dihydroorotate dehydrogenase. The results presented here may be a good starting point for the development of alternative treatments for Chagas disease and for understanding the mechanism of naphthoimidazoles in T. cruzi.
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Affiliation(s)
- Ana Cristina S Bombaça
- Laboratório de Biologia Celular, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Leonardo A Silva
- Instituto de Química, Universidade Federal Rural do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Otávio Augusto Chaves
- Instituto de Química, Universidade Federal Rural do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Lorrainy S da Silva
- Instituto de Química, Universidade Federal Rural do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Juliana M C Barbosa
- Laboratório de Biologia Celular, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Ari M da Silva
- Instituto de Pesquisa em Produtos Naturais, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Aurélio B B Ferreira
- Instituto de Química, Universidade Federal Rural do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Rubem F S Menna-Barreto
- Laboratório de Biologia Celular, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil.
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8
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Sato D, Hartuti ED, Inaoka DK, Sakura T, Amalia E, Nagahama M, Yoshioka Y, Tsuji N, Nozaki T, Kita K, Harada S, Matsubayashi M, Shiba T. Structural and Biochemical Features of Eimeria tenella Dihydroorotate Dehydrogenase, a Potential Drug Target. Genes (Basel) 2020; 11:genes11121468. [PMID: 33297567 PMCID: PMC7762340 DOI: 10.3390/genes11121468] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 12/03/2020] [Accepted: 12/04/2020] [Indexed: 12/23/2022] Open
Abstract
Dihydroorotate dehydrogenase (DHODH) is a mitochondrial monotopic membrane protein that plays an essential role in the pyrimidine de novo biosynthesis and electron transport chain pathways. In Eimeria tenella, an intracellular apicomplexan parasite that causes the most severe form of chicken coccidiosis, the activity of pyrimidine salvage pathway at the intracellular stage is negligible and it relies on the pyrimidine de novo biosynthesis pathway. Therefore, the enzymes of the de novo pathway are considered potential drug target candidates for the design of compounds with activity against this parasite. Although, DHODHs from E. tenella (EtDHODH), Plasmodium falciparum (PfDHODH), and human (HsDHODH) show distinct sensitivities to classical DHODH inhibitors, in this paper, we identify ferulenol as a potent inhibitor of both EtDHODH and HsDHODH. Additionally, we report the crystal structures of EtDHODH and HsDHODH in the absence and presence of ferulenol. Comparison of these enzymes showed that despite similar overall structures, the EtDHODH has a long insertion in the N-terminal helix region that assumes a disordered configuration. In addition, the crystal structures revealed that the ferulenol binding pocket of EtDHODH is larger than that of HsDHODH. These differences can be explored to accelerate structure-based design of inhibitors specifically targeting EtDHODH.
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Affiliation(s)
- Dan Sato
- Department of Applied Biology, Graduate School of Science Technology, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan; (D.S.); (M.N.); (Y.Y.); (S.H.)
| | - Endah Dwi Hartuti
- Department of Parasitology, Institute of Tropical Medicine (NEKKEN), Nagasaki University, 1-12-4 Sakamoto, Nagasaki 852-8523, Japan;
| | - Daniel Ken Inaoka
- Department of Molecular Infection Dynamics, Institute of Tropical Medicine (NEKKEN), Nagasaki University, 1-12-4 Sakamoto, Nagasaki 852-8523, Japan;
- School of Tropical Medicine and Global Health, Nagasaki University, 1-12-4 Sakamoto, Nagasaki 852-8523, Japan;
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan; (E.A.); (T.N.)
- Correspondence: (D.K.I.); (T.S.); Tel.: +81-95-819-7230 (D.K.I.); Tel./Fax: +81-75-724-7541 (T.S.)
| | - Takaya Sakura
- Department of Molecular Infection Dynamics, Institute of Tropical Medicine (NEKKEN), Nagasaki University, 1-12-4 Sakamoto, Nagasaki 852-8523, Japan;
- School of Tropical Medicine and Global Health, Nagasaki University, 1-12-4 Sakamoto, Nagasaki 852-8523, Japan;
| | - Eri Amalia
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan; (E.A.); (T.N.)
| | - Madoka Nagahama
- Department of Applied Biology, Graduate School of Science Technology, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan; (D.S.); (M.N.); (Y.Y.); (S.H.)
| | - Yukina Yoshioka
- Department of Applied Biology, Graduate School of Science Technology, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan; (D.S.); (M.N.); (Y.Y.); (S.H.)
| | - Naotoshi Tsuji
- Department of Parasitology, Kitasato University School of Medicine, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa 252-0374, Japan;
| | - Tomoyoshi Nozaki
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan; (E.A.); (T.N.)
| | - Kiyoshi Kita
- School of Tropical Medicine and Global Health, Nagasaki University, 1-12-4 Sakamoto, Nagasaki 852-8523, Japan;
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan; (E.A.); (T.N.)
- Department of Host-Defense Biochemistry, Institute of Tropical Medicine (NEKKEN), Nagasaki University, 1-12-4 Sakamoto, Nagasaki 852-8523, Japan
| | - Shigeharu Harada
- Department of Applied Biology, Graduate School of Science Technology, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan; (D.S.); (M.N.); (Y.Y.); (S.H.)
| | - Makoto Matsubayashi
- Division of Veterinary Science, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, 1-58 Rinku Orai Kita, Izumisano, Osaka 598-8531, Japan;
| | - Tomoo Shiba
- Department of Applied Biology, Graduate School of Science Technology, Kyoto Institute of Technology, Matsugasaki, Sakyo-ku, Kyoto 606-8585, Japan; (D.S.); (M.N.); (Y.Y.); (S.H.)
- Correspondence: (D.K.I.); (T.S.); Tel.: +81-95-819-7230 (D.K.I.); Tel./Fax: +81-75-724-7541 (T.S.)
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Repositioned Drugs for Chagas Disease Unveiled via Structure-Based Drug Repositioning. Int J Mol Sci 2020; 21:ijms21228809. [PMID: 33233837 PMCID: PMC7699892 DOI: 10.3390/ijms21228809] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 11/08/2020] [Accepted: 11/16/2020] [Indexed: 12/18/2022] Open
Abstract
Chagas disease, caused by the parasite Trypanosoma cruzi, affects millions of people in South America. The current treatments are limited, have severe side effects, and are only partially effective. Drug repositioning, defined as finding new indications for already approved drugs, has the potential to provide new therapeutic options for Chagas. In this work, we conducted a structure-based drug repositioning approach with over 130,000 3D protein structures to identify drugs that bind therapeutic Chagas targets and thus represent potential new Chagas treatments. The screening yielded over 500 molecules as hits, out of which 38 drugs were prioritized following a rigorous filtering process. About half of the latter were already known to have trypanocidal activity, while the others are novel to Chagas disease. Three of the new drug candidates—ciprofloxacin, naproxen, and folic acid—showed a growth inhibitory activity in the micromolar range when tested ex vivo on T. cruzi trypomastigotes, validating the prediction. We show that our drug repositioning approach is able to pinpoint relevant drug candidates at a fraction of the time and cost of a conventional screening. Furthermore, our results demonstrate the power and potential of structure-based drug repositioning in the context of neglected tropical diseases where the pharmaceutical industry has little financial interest in the development of new drugs.
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10
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Investigating the amino acid sequences of membrane bound dihydroorotate:quinone oxidoreductases (DHOQOs): Structural and functional implications. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2020; 1862:148321. [PMID: 32991846 DOI: 10.1016/j.bbabio.2020.148321] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 09/14/2020] [Accepted: 09/23/2020] [Indexed: 12/26/2022]
Abstract
Dihydroorotate:quinone oxidoreductases (DHOQOs) are membrane bound enzymes responsible for oxidizing dihydroorotate (DHO) to orotate with concomitant reduction of quinone to quinol. They have FMN as prosthetic group and are part of the monotopic quinone reductase superfamily. These enzymes are also members of the dihydroorotate dehydrogenases (DHODHs) family, which besides membrane bound DHOQOs, class 2, includes soluble enzymes which reduce either NAD+ or fumarate, class 1. As key enzymes in both the de novo pyrimidine biosynthetic pathway as well as in the energetic metabolism, inhibitors of DHOQOs have been investigated as leads for therapeutics in cancer, immunological disorders and bacterial/viral infections. This work is a thorough bioinformatic approach on the structural conservation and taxonomic distribution of DHOQOs. We explored previously established structural/functional hallmarks of these enzymes, while searching for uncharacterized common elements. We also discuss the cellular role of DHOQOs and organize the identified protein sequences within six sub-classes 2A to 2F, according to their taxonomic origin and sequence traits. We concluded that DHOQOs are present in Archaea, Eukarya and Bacteria, including the first recognition in Gram-positive organisms. DHOQOs can be the single dihydroorotate dehydrogenase encoded in the genome of a species, or they can coexist with other DHODHs, as the NAD+ or fumarate reducing enzymes. Furthermore, we show that the type of catalytic base present in the active site is not an absolute criterium to distinguish between class 1 and class 2 enzymes. We propose the existence of a quinone binding motif ("ExAH") adjacent to a hydrophobic cavity present in the membrane interacting N-terminal domain.
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11
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Dihydroorotate dehydrogenase inhibitors in anti-infective drug research. Eur J Med Chem 2019; 183:111681. [PMID: 31557612 DOI: 10.1016/j.ejmech.2019.111681] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Revised: 08/01/2019] [Accepted: 09/05/2019] [Indexed: 01/08/2023]
Abstract
Pyrimidines are essential for the cell survival and proliferation of living parasitic organisms, such as Helicobacter pylori, Plasmodium falciparum and Schistosoma mansoni, that are able to impact upon human health. Pyrimidine building blocks, in human cells, are synthesised via both de novo biosynthesis and salvage pathways, the latter of which is an effective way of recycling pre-existing nucleotides. As many parasitic organisms lack pyrimidine salvage pathways for pyrimidine nucleotides, blocking de novo biosynthesis is seen as an effective therapeutic means to selectively target the parasite without effecting the human host. Dihydroorotate dehydrogenase (DHODH), which is involved in the de novo biosynthesis of pyrimidines, is a validated target for anti-infective drug research. Recent advances in the DHODH microorganism field are discussed herein, as is the potential for the development of DHODH-targeted therapeutics.
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Shiba T, Inaoka DK, Takahashi G, Tsuge C, Kido Y, Young L, Ueda S, Balogun EO, Nara T, Honma T, Tanaka A, Inoue M, Saimoto H, Harada S, Moore AL, Kita K. Insights into the ubiquinol/dioxygen binding and proton relay pathways of the alternative oxidase. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2019; 1860:375-382. [PMID: 30910528 DOI: 10.1016/j.bbabio.2019.03.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 03/20/2019] [Indexed: 12/21/2022]
Abstract
The alternative oxidase (AOX) is a monotopic diiron carboxylate protein which catalyzes the four-electron reduction of dioxygen to water by ubiquinol. Although we have recently determined the crystal structure of Trypanosoma brucei AOX (TAO) in the presence and absence of ascofuranone (AF) derivatives (which are potent mixed type inhibitors) the mechanism by which ubiquinol and dioxygen binds to TAO remain inconclusive. In this article, ferulenol was identified as the first competitive inhibitor of AOX which has been used to probe the binding of ubiquinol. Surface plasmon resonance reveals that AF is a quasi-irreversible inhibitor of TAO whilst ferulenol binding is completely reversible. The structure of the TAO-ferulenol complex, determined at 2.7 Å, provided insights into ubiquinol binding and has also identified a potential dioxygen molecule bound in a side-on conformation to the diiron center for the first time.
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Affiliation(s)
- Tomoo Shiba
- Department of Applied Biology, Graduate School of Science and Technology, Kyoto Institute of Technology, Sakyo-ku, Matsugasaki, Kyoto 606-8585, Japan.
| | - Daniel Ken Inaoka
- School of Tropical Medicine and Global Health, Nagasaki University, Sakamoto 1-12-4, Nagasaki 852-8523, Japan; Department of Host-Defense Biochemistry, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Sakamoto 1-12-4, Nagasaki 852-8523, Japan; Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Hongo 7-3-1, Tokyo 113-0033, Japan.
| | - Gen Takahashi
- Department of Applied Biology, Graduate School of Science and Technology, Kyoto Institute of Technology, Sakyo-ku, Matsugasaki, Kyoto 606-8585, Japan
| | - Chiaki Tsuge
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Hongo 7-3-1, Tokyo 113-0033, Japan
| | - Yasutoshi Kido
- School of Tropical Medicine and Global Health, Nagasaki University, Sakamoto 1-12-4, Nagasaki 852-8523, Japan; Department of Parasitology, Graduate School of Medicine, Osaka City University, Abeno-ku, Asahimachi 1-4-3, Osaka 545-8585, Japan
| | - Luke Young
- Biochemistry and Biomedicine, School of Life Sciences, University of Sussex, Falmer, Brighton, BN1 9QG, UK
| | - Satoshi Ueda
- Department of Applied Biology, Graduate School of Science and Technology, Kyoto Institute of Technology, Sakyo-ku, Matsugasaki, Kyoto 606-8585, Japan
| | - Emmanuel Oluwadare Balogun
- Department of Applied Biology, Graduate School of Science and Technology, Kyoto Institute of Technology, Sakyo-ku, Matsugasaki, Kyoto 606-8585, Japan; Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Hongo 7-3-1, Tokyo 113-0033, Japan; Department of Biochemistry, Ahmadu Bello University, Zaria 2222, Nigeria
| | - Takeshi Nara
- Department of Molecular and Cellular Parasitology, Juntendo University School of Medicine, Bunkyo-ku, Hongo 2-1-1, Tokyo, 113-8421, Japan
| | - Teruki Honma
- Systems and Structural Biology Center, RIKEN, Tsurumi, Suehiro 1-7-22, Yokohama, Kanagawa 230-0045, Japan
| | - Akiko Tanaka
- Systems and Structural Biology Center, RIKEN, Tsurumi, Suehiro 1-7-22, Yokohama, Kanagawa 230-0045, Japan
| | - Masayuki Inoue
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Bunkyo-ku, Hongo 7-3-1, Tokyo 113-0033, Japan
| | - Hiroyuki Saimoto
- Department of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, Koyamacho-Minami 4, Tottori 680-8552, Japan
| | - Shigeharu Harada
- Department of Applied Biology, Graduate School of Science and Technology, Kyoto Institute of Technology, Sakyo-ku, Matsugasaki, Kyoto 606-8585, Japan
| | - Anthony L Moore
- Biochemistry and Biomedicine, School of Life Sciences, University of Sussex, Falmer, Brighton, BN1 9QG, UK
| | - Kiyoshi Kita
- School of Tropical Medicine and Global Health, Nagasaki University, Sakamoto 1-12-4, Nagasaki 852-8523, Japan; Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, Bunkyo-ku, Hongo 7-3-1, Tokyo 113-0033, Japan; Department of Host-Defense Biochemistry, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Sakamoto 1-12-4, Nagasaki 852-8523, Japan
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Novel Characteristics of Mitochondrial Electron Transport Chain from Eimeria tenella. Genes (Basel) 2019; 10:genes10010029. [PMID: 30626105 PMCID: PMC6356742 DOI: 10.3390/genes10010029] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 12/28/2018] [Accepted: 12/28/2018] [Indexed: 12/26/2022] Open
Abstract
Eimeria tenella is an intracellular apicomplexan parasite, which infects cecal epithelial cells from chickens and causes hemorrhagic diarrhea and eventual death. We have previously reported the comparative RNA sequence analysis of the E. tenella sporozoite stage between virulent and precocious strains and showed that the expression of several genes involved in mitochondrial electron transport chain (ETC), such as type II NADH dehydrogenase (NDH-2), complex II (succinate:quinone oxidoreductase), malate:quinone oxidoreductase (MQO), and glycerol-3-phosphate dehydrogenase (G3PDH), were upregulated in virulent strain. To study E. tenella mitochondrial ETC in detail, we developed a reproducible method for preparation of mitochondria-rich fraction from sporozoites, which maintained high specific activities of dehydrogenases, such as NDH-2 followed by G3PDH, MQO, complex II, and dihydroorotate dehydrogenase (DHODH). Of particular importance, we showed that E. tenella sporozoite mitochondria possess an intrinsic ability to perform fumarate respiration (via complex II) in addition to the classical oxygen respiration (via complexes III and IV). Further analysis by high-resolution clear native electrophoresis, activity staining, and nano-liquid chromatography tandem-mass spectrometry (nano-LC-MS/MS) provided evidence of a mitochondrial complex II-III-IV supercomplex. Our analysis suggests that complex II from E. tenella has biochemical features distinct to known orthologues and is a potential target for the development of new anticoccidian drugs.
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High-through identification of T cell-specific phage-exposed mimotopes using PBMCs from tegumentary leishmaniasis patients and their use as vaccine candidates against Leishmania amazonensis infection. Parasitology 2018; 146:322-332. [PMID: 30198459 DOI: 10.1017/s0031182018001403] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
In the current study, phage-exposed mimotopes as targets against tegumentary leishmaniasis (TL) were selected by means of bio-panning cycles employing sera of TL patients and healthy subjects, besides the immune stimulation of peripheral blood mononuclear cells (PBMCs) collected from untreated and treated TL patients and healthy subjects. The clones were evaluated regarding their specific interferon-γ (IFN-γ) and interleukin-4 (IL-4) production in the in vitro cultures, and selectivity and specificity values were calculated, and those presenting the best results were selected for the in vivo experiments. Two clones, namely A4 and A8, were identified and used in immunization protocols from BALB/c mice to protect against Leishmania amazonensis infection. Results showed a polarized Th1 response generated after vaccination, being based on significantly higher levels of IFN-γ, IL-2, IL-12, tumour necrosis factor-α (TNF-α) and granulocyte-macrophage colony-stimulating factor (GM-CSF); which were associated with lower production of specific IL-4, IL-10 and immunoglobulin G1 (IgG1) antibodies. Vaccinated mice presented significant reductions in the parasite load in the infected tissue and distinct organs, when compared with controls. In conclusion, we presented a strategy to identify new mimotopes able to induce Th1 response in PBMCs from TL patients and healthy subjects, and that were successfully used to protect against L. amazonensis infection.
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Miyazaki Y, Inaoka DK, Shiba T, Saimoto H, Sakura T, Amalia E, Kido Y, Sakai C, Nakamura M, Moore AL, Harada S, Kita K. Selective Cytotoxicity of Dihydroorotate Dehydrogenase Inhibitors to Human Cancer Cells Under Hypoxia and Nutrient-Deprived Conditions. Front Pharmacol 2018; 9:997. [PMID: 30233375 PMCID: PMC6131557 DOI: 10.3389/fphar.2018.00997] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 08/13/2018] [Indexed: 12/15/2022] Open
Abstract
Human dihydroorotate dehydrogenase (HsDHODH) is a key enzyme of pyrimidine de novo biosynthesis pathway. It is located on the mitochondrial inner membrane and contributes to the respiratory chain by shuttling electrons to the ubiquinone pool. We have discovered ascofuranone (1), a natural compound produced by Acremonium sclerotigenum, and its derivatives are a potent class of HsDHODH inhibitors. We conducted a structure–activity relationship study and have identified functional groups of 1 that are essential for the inhibition of HsDHODH enzymatic activity. Furthermore, the binding mode of 1 and its derivatives to HsDHODH was demonstrated by co-crystallographic analysis and we show that these inhibitors bind at the ubiquinone binding site. In addition, the cytotoxicities of 1 and its potent derivatives 7, 8, and 9 were studied using human cultured cancer cells. Interestingly, they showed selective and strong cytotoxicity to cancer cells cultured under microenvironment (hypoxia and nutrient-deprived) conditions. The selectivity ratio of 8 under this microenvironment show the most potent inhibition which was over 1000-fold higher compared to that under normal culture condition. Our studies suggest that under microenvironment conditions, cancer cells heavily depend on the pyrimidine de novo biosynthesis pathway. We also provide the first evidence that 1 and its derivatives are potential lead candidates for drug development which target the HsDHODH of cancer cells living under a tumor microenvironment.
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Affiliation(s)
- Yukiko Miyazaki
- School of Tropical Medicine and Global Health, Nagasaki University, Nagasaki, Japan.,Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Daniel K Inaoka
- School of Tropical Medicine and Global Health, Nagasaki University, Nagasaki, Japan.,Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.,Department of Host-Defense Biochemistry, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki, Japan
| | - Tomoo Shiba
- Department of Applied Biology, Graduate School of Science and Technology, Kyoto Institute of Technology, Kyoto, Japan
| | - Hiroyuki Saimoto
- Department of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, Tottori, Japan
| | - Takaya Sakura
- School of Tropical Medicine and Global Health, Nagasaki University, Nagasaki, Japan
| | - Eri Amalia
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Yasutoshi Kido
- School of Tropical Medicine and Global Health, Nagasaki University, Nagasaki, Japan
| | - Chika Sakai
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Mari Nakamura
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Anthony L Moore
- Biochemistry and Medicine, School of Life Sciences, University of Sussex, Brighton, United Kingdom
| | - Shigeharu Harada
- Department of Applied Biology, Graduate School of Science and Technology, Kyoto Institute of Technology, Kyoto, Japan
| | - Kiyoshi Kita
- School of Tropical Medicine and Global Health, Nagasaki University, Nagasaki, Japan.,Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.,Department of Host-Defense Biochemistry, Institute of Tropical Medicine (NEKKEN), Nagasaki University, Nagasaki, Japan
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16
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Maklashina E, Rajagukguk S, Iverson TM, Cecchini G. The unassembled flavoprotein subunits of human and bacterial complex II have impaired catalytic activity and generate only minor amounts of ROS. J Biol Chem 2018; 293:7754-7765. [PMID: 29610278 PMCID: PMC5961047 DOI: 10.1074/jbc.ra118.001977] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Revised: 03/28/2018] [Indexed: 01/28/2023] Open
Abstract
Complex II (SdhABCD) is a membrane-bound component of mitochondrial and bacterial electron transport chains, as well as of the TCA cycle. In this capacity, it catalyzes the reversible oxidation of succinate. SdhABCD contains the SDHA protein harboring a covalently bound FAD redox center and the iron-sulfur protein SDHB, containing three distinct iron-sulfur centers. When assembly of this complex is compromised, the flavoprotein SDHA may accumulate in the mitochondrial matrix or bacterial cytoplasm. Whether the unassembled SDHA has any catalytic activity, for example in succinate oxidation, fumarate reduction, reactive oxygen species (ROS) generation, or other off-pathway reactions, is not known. Therefore, here we investigated whether unassembled Escherichia coli SdhA flavoprotein, its homolog fumarate reductase (FrdA), and the human SDHA protein have succinate oxidase or fumarate reductase activity and can produce ROS. Using recombinant expression in E. coli, we found that the free flavoproteins from these divergent biological sources have inherently low catalytic activity and generate little ROS. These results suggest that the iron-sulfur protein SDHB in complex II is necessary for robust catalytic activity. Our findings are consistent with those reported for single-subunit flavoprotein homologs that are not associated with iron-sulfur or heme partner proteins.
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Affiliation(s)
- Elena Maklashina
- From the Molecular Biology Division, San Francisco Veterans Affairs Health Care System, San Francisco, California 94121, ,the Department of Biochemistry & Biophysics, University of California, San Francisco, California 94158, and
| | - Sany Rajagukguk
- From the Molecular Biology Division, San Francisco Veterans Affairs Health Care System, San Francisco, California 94121
| | - T. M. Iverson
- the Departments of Pharmacology and ,Biochemistry, ,the Center for Structural Biology, and ,the Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, Tennessee 37232
| | - Gary Cecchini
- From the Molecular Biology Division, San Francisco Veterans Affairs Health Care System, San Francisco, California 94121, ,the Department of Biochemistry & Biophysics, University of California, San Francisco, California 94158, and , Recipient of Senior Research Career Scientist Award IK6BX004215 from the Department of Veterans Affairs. To whom correspondence should be addressed:
Molecular Biology Division (151-S), San Francisco Veterans Affairs Healthcare System, 4150 Clement St., San Francisco, CA 94121. Tel.:
415-221-4810, Ext. 24416; E-mail:
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17
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Kubota T, Tani O, Yamaguchi T, Namatame I, Sakashita H, Furukawa K, Yamasaki K. Crystal structures of FMN-bound and FMN-free forms of dihydroorotate dehydrogenase from Trypanosoma brucei. FEBS Open Bio 2018; 8:680-691. [PMID: 29632820 PMCID: PMC5881531 DOI: 10.1002/2211-5463.12403] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Revised: 02/08/2018] [Accepted: 02/08/2018] [Indexed: 01/29/2023] Open
Abstract
Dihydroorotate dehydrogenase (DHODH) is a flavin‐binding enzyme essential for pyrimidine biosynthesis, which converts dihydroorotate to orotate. Three‐dimensional structures of cytosolic DHODH of parasitic protozoa are of interest in drug discovery for neglected tropical diseases, especially because these enzymes possess significantly different structural and functional properties from the membrane‐associated human enzyme. The existing crystal structures of the flavin mononucleotide (FMN)‐bound DHODHs reveal a number of interactions stabilizing FMN. However, to understand the binding mechanism correctly, it is necessary to compare the structures of the FMN‐bound and FMN‐free forms, because the protein moiety of the former is not necessarily the same as the latter. Here, we prepared the FMN‐free DHODH of Trypanosoma brucei using an Escherichia coli overexpression system. Although this apoform lacks enzymatic activity, simple incubation with FMN activated the enzyme. It was stable enough to be crystallized, enabling us to determine its structure by X‐ray crystallography at 1.6 Å resolution. We also determined the FMN‐bound form at 1.8 Å resolution. Although the two structures have essentially the same scaffold, we observed flipping of a peptide‐bond plane in the vicinity of the FMN‐binding site, accompanied by an alternative hydrogen‐bonding pattern. Comparisons of B factors of the protein main chain revealed that binding of FMN decreased flexibility of most of the residues at the FMN‐binding site, but increased flexibility of a lid‐like loop structure over the active center. This increase was ascribed to a conformational change in an FMN‐contacting residue, Asn195, which induced a rearrangement of a hydrogen‐bond network of the residues comprising the lid.
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Affiliation(s)
- Tomomi Kubota
- Biomedical Research Institute National Institute of Advanced Industrial Science and Technology (AIST) Tsukuba Japan
| | - Osamu Tani
- Biomedical Research Institute National Institute of Advanced Industrial Science and Technology (AIST) Tsukuba Japan
| | | | | | - Hitoshi Sakashita
- Biomedical Research Institute National Institute of Advanced Industrial Science and Technology (AIST) Tsukuba Japan
| | - Koji Furukawa
- Biomedical Research Institute National Institute of Advanced Industrial Science and Technology (AIST) Tsukuba Japan
| | - Kazuhiko Yamasaki
- Biomedical Research Institute National Institute of Advanced Industrial Science and Technology (AIST) Tsukuba Japan
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18
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Fresh insights into the pyrimidine metabolism in the trypanosomatids. Parasit Vectors 2018; 11:87. [PMID: 29422065 PMCID: PMC5803862 DOI: 10.1186/s13071-018-2660-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Accepted: 01/18/2018] [Indexed: 11/26/2022] Open
Abstract
The trypanosomatid parasites continue their killing spree resulting in significant annual mortality due to the lack of effective treatments and the prominence of these diseases in poorer countries. These dimorphic parasites thrive unchecked in the host system, outsmarting the immune mechanisms. An understanding of biology of these parasitic forms will help in the management and elimination of these fatal diseases. Investigation of various metabolic pathways in these parasites has shed light in the understanding of the unique biology of the trypansomatids. An understanding of these pathways have helped in tracing the soft targets in the metabolic pathways, which could be used as effective drug targets which would further impact the therupeutic implications. Pyrimidine pathway is a vital metabolic pathway which yields in the formation of pyrimidines, which are then integrated in nucleic acids (DNA and RNA) in sugars (UDP sugars) and lipids (CDP lipids). A wealth of data and information has been generated in the past decades by in-depth analyses of pyrimidine pathway in the trypanosomatid parasites, which can aid in the identification of anomalies between the parasitic and host counterpart which could be further harnessed to develop therapeutic interventions for the treatment of parasitic diseases. This review presents an updated and comprehensive detailing of the pyrimidine metabolism in the trypansomatids, their uniqueness and their distinctions, and its possible outcomes that would aid in the eradication of these parasitic diseases.
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Hartuti ED, Inaoka DK, Komatsuya K, Miyazaki Y, Miller RJ, Xinying W, Sadikin M, Prabandari EE, Waluyo D, Kuroda M, Amalia E, Matsuo Y, Nugroho NB, Saimoto H, Pramisandi A, Watanabe YI, Mori M, Shiomi K, Balogun EO, Shiba T, Harada S, Nozaki T, Kita K. Biochemical studies of membrane bound Plasmodium falciparum mitochondrial L-malate:quinone oxidoreductase, a potential drug target. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2017; 1859:191-200. [PMID: 29269266 DOI: 10.1016/j.bbabio.2017.12.004] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Revised: 12/13/2017] [Accepted: 12/16/2017] [Indexed: 11/30/2022]
Abstract
Plasmodium falciparum is an apicomplexan parasite that causes the most severe malaria in humans. Due to a lack of effective vaccines and emerging of drug resistance parasites, development of drugs with novel mechanisms of action and few side effects are imperative. To this end, ideal drug targets are those essential to parasite viability as well as absent in their mammalian hosts. The mitochondrial electron transport chain (ETC) of P. falciparum is one source of such potential targets because enzymes, such as L-malate:quinone oxidoreductase (PfMQO), in this pathway are absent humans. PfMQO catalyzes the oxidation of L-malate to oxaloacetate and the simultaneous reduction of ubiquinone to ubiquinol. It is a membrane protein, involved in three pathways (ETC, the tricarboxylic acid cycle and the fumarate cycle) and has been shown to be essential for parasite survival, at least, in the intra-erythrocytic asexual stage. These findings indicate that PfMQO would be a valuable drug target for development of antimalarial with novel mechanism of action. Up to this point in time, difficulty in producing active recombinant mitochondrial MQO has hampered biochemical characterization and targeted drug discovery with MQO. Here we report for the first time recombinant PfMQO overexpressed in bacterial membrane and the first biochemical study. Furthermore, about 113 compounds, consisting of ubiquinone binding site inhibitors and antiparasitic agents, were screened resulting in the discovery of ferulenol as a potent PfMQO inhibitor. Finally, ferulenol was shown to inhibit parasite growth and showed strong synergism in combination with atovaquone, a well-described anti-malarial and bc1 complex inhibitor.
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Affiliation(s)
- Endah Dwi Hartuti
- Master program of Biomedical Science, Faculty of Medicine, University of Indonesia, Indonesia; Biotech Center, Agency for the Assessment and Application of Technology, Jakarta, Indonesia
| | - Daniel Ken Inaoka
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan; School of Tropical Medicine and Global Health, Nagasaki University, Nagasaki, Japan.
| | - Keisuke Komatsuya
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Yukiko Miyazaki
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Russell J Miller
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Wang Xinying
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan; School of Tropical Medicine and Global Health, Nagasaki University, Nagasaki, Japan
| | - Mohamad Sadikin
- Department of Biochemistry & Molecular Biology, Faculty of Medicine, University of Indonesia, Jakarta, Indonesia
| | | | - Danang Waluyo
- Biotech Center, Agency for the Assessment and Application of Technology, Jakarta, Indonesia
| | - Marie Kuroda
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Eri Amalia
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Yuichi Matsuo
- School of Tropical Medicine and Global Health, Nagasaki University, Nagasaki, Japan
| | - Nuki B Nugroho
- Biotech Center, Agency for the Assessment and Application of Technology, Jakarta, Indonesia
| | - Hiroyuki Saimoto
- Department of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, Tottori, Japan
| | - Amila Pramisandi
- Biotech Center, Agency for the Assessment and Application of Technology, Jakarta, Indonesia; Graduate School of Infection Control Sciences, Kitasato University, Tokyo, Japan
| | - Yoh-Ichi Watanabe
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Mihoko Mori
- Graduate School of Infection Control Sciences, Kitasato University, Tokyo, Japan
| | - Kazuro Shiomi
- Graduate School of Infection Control Sciences, Kitasato University, Tokyo, Japan
| | - Emmanuel Oluwadare Balogun
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan; Department of Biochemistry, Ahmadu Bello University, Zaria, Nigeria
| | - Tomoo Shiba
- Department of Applied Biology, Graduate School of Science Technology, Kyoto Institute of Technology, Kyoto, Japan
| | - Shigeharu Harada
- Department of Applied Biology, Graduate School of Science Technology, Kyoto Institute of Technology, Kyoto, Japan
| | - Tomoyoshi Nozaki
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Kiyoshi Kita
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan; School of Tropical Medicine and Global Health, Nagasaki University, Nagasaki, Japan
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Wachsmuth LM, Johnson MG, Gavenonis J. Essential multimeric enzymes in kinetoplastid parasites: A host of potentially druggable protein-protein interactions. PLoS Negl Trop Dis 2017; 11:e0005720. [PMID: 28662026 PMCID: PMC5507555 DOI: 10.1371/journal.pntd.0005720] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Revised: 07/12/2017] [Accepted: 06/16/2017] [Indexed: 12/18/2022] Open
Abstract
Parasitic diseases caused by kinetoplastid parasites of the genera Trypanosoma and Leishmania are an urgent public health crisis in the developing world. These closely related species possess a number of multimeric enzymes in highly conserved pathways involved in vital functions, such as redox homeostasis and nucleotide synthesis. Computational alanine scanning of these protein-protein interfaces has revealed a host of potentially ligandable sites on several established and emerging anti-parasitic drug targets. Analysis of interfaces with multiple clustered hotspots has suggested several potentially inhibitable protein-protein interactions that may have been overlooked by previous large-scale analyses focusing solely on secondary structure. These protein-protein interactions provide a promising lead for the development of new peptide and macrocycle inhibitors of these enzymes.
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Affiliation(s)
- Leah M. Wachsmuth
- Department of Chemistry, Dickinson College, Carlisle, Pennsylvania, United States of America
| | - Meredith G. Johnson
- Department of Chemistry, Dickinson College, Carlisle, Pennsylvania, United States of America
| | - Jason Gavenonis
- Department of Chemistry, Dickinson College, Carlisle, Pennsylvania, United States of America
- * E-mail:
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21
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Reis RAG, Calil FA, Feliciano PR, Pinheiro MP, Nonato MC. The dihydroorotate dehydrogenases: Past and present. Arch Biochem Biophys 2017; 632:175-191. [PMID: 28666740 DOI: 10.1016/j.abb.2017.06.019] [Citation(s) in RCA: 98] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Revised: 06/23/2017] [Accepted: 06/26/2017] [Indexed: 01/24/2023]
Abstract
The flavoenzyme dihydroorotate dehydrogenase catalyzes the stereoselective oxidation of (S)-dihydroorotate to orotate in the fourth of the six conserved enzymatic reactions involved in the de novo pyrimidine biosynthetic pathway. Inhibition of pyrimidine metabolism by selectively targeting DHODHs has been exploited in the development of new therapies against cancer, immunological disorders, bacterial and viral infections, and parasitic diseases. Through a chronological narrative, this review summarizes the efforts of the scientific community to achieve our current understanding of structural and biochemical properties of DHODHs. It also attempts to describe the latest advances in medicinal chemistry for therapeutic development based on the selective inhibition of DHODH, including an overview of the experimental techniques used for ligand screening during the process of drug discovery.
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Affiliation(s)
- Renata A G Reis
- Department of Chemistry, Georgia State University, Atlanta, GA 30302, United States
| | - Felipe Antunes Calil
- Laboratório de Cristalografia de Proteínas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, 14040-903, Brazil
| | - Patricia Rosa Feliciano
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
| | - Matheus Pinto Pinheiro
- Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Sao Paulo, 13083-970, Brazil
| | - M Cristina Nonato
- Laboratório de Cristalografia de Proteínas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, 14040-903, Brazil.
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22
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Inaoka DK, Iida M, Hashimoto S, Tabuchi T, Kuranaga T, Balogun EO, Honma T, Tanaka A, Harada S, Nara T, Kita K, Inoue M. Design and synthesis of potent substrate-based inhibitors of the Trypanosoma cruzi dihydroorotate dehydrogenase. Bioorg Med Chem 2017; 25:1465-1470. [DOI: 10.1016/j.bmc.2017.01.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Accepted: 01/06/2017] [Indexed: 11/27/2022]
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23
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The Open Form Inducer Approach for Structure-Based Drug Design. PLoS One 2016; 11:e0167078. [PMID: 27893848 PMCID: PMC5125662 DOI: 10.1371/journal.pone.0167078] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Accepted: 11/08/2016] [Indexed: 01/07/2023] Open
Abstract
Many open form (OF) structures of drug targets were obtained a posteriori by analysis of co-crystals with inhibitors. Therefore, obtaining the OF structure of a drug target a priori will accelerate development of potent inhibitors. In addition to its small active site, Trypanosoma cruzi dihydroorotate dehydrogenase (TcDHODH) is fully functional in its monomeric form, making drug design approaches targeting the active site and protein-protein interactions unrealistic. Therefore, a novel a priori approach was developed to determination the TcDHODH active site in OF. This approach consists of generating an "OF inducer" (predicted in silico) to bind the target and cause steric repulsion with flexible regions proximal to the active site that force it open. We provide the first proof-of-concept of this approach by predicting and crystallizing TcDHODH in complex with an OF inducer, thereby obtaining the OF a priori with its subsequent use in designing potent and selective inhibitors. Fourteen co-crystal structures of TcDHODH with the designed inhibitors are presented herein. This approach has potential to encourage drug design against diseases where the molecular targets are such difficult proteins possessing small AS volume. This approach can be extended to study open/close conformation of proteins in general, the identification of allosteric pockets and inhibitors for other drug targets where conventional drug design approaches are not applicable, as well as the effective exploitation of the increasing number of protein structures deposited in Protein Data Bank.
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24
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Ogungbe IV, Setzer WN. The Potential of Secondary Metabolites from Plants as Drugs or Leads against Protozoan Neglected Diseases-Part III: In-Silico Molecular Docking Investigations. Molecules 2016; 21:E1389. [PMID: 27775577 PMCID: PMC6274513 DOI: 10.3390/molecules21101389] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Revised: 10/06/2016] [Accepted: 10/12/2016] [Indexed: 12/11/2022] Open
Abstract
Malaria, leishmaniasis, Chagas disease, and human African trypanosomiasis continue to cause considerable suffering and death in developing countries. Current treatment options for these parasitic protozoal diseases generally have severe side effects, may be ineffective or unavailable, and resistance is emerging. There is a constant need to discover new chemotherapeutic agents for these parasitic infections, and natural products continue to serve as a potential source. This review presents molecular docking studies of potential phytochemicals that target key protein targets in Leishmania spp., Trypanosoma spp., and Plasmodium spp.
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Affiliation(s)
- Ifedayo Victor Ogungbe
- Department of Chemistry and Biochemistry, Jackson State University, Jackson, MS 39217, USA.
| | - William N Setzer
- Department of Chemistry, University of Alabama in Huntsville, Huntsville, AL 35899, USA.
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25
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The mechanistic study of Leishmania major dihydro-orotate dehydrogenase based on steady- and pre-steady-state kinetic analysis. Biochem J 2016; 473:651-60. [DOI: 10.1042/bj20150921] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Accepted: 12/11/2015] [Indexed: 11/17/2022]
Abstract
Leishmania major dihydro-orotate dehydrogenase (DHODHLm) oxidizes dihydro-orotate to orotate (ORO) in the de novo pyrimidine biosynthetic pathway. The enzyme reaction mechanism was elucidated by steady- and pre-steady-state kinetics. ORO release was found to be the rate-limiting step in the overall catalysis.
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26
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Alves CN, Silva JRA, Roitberg AE. Insights into the mechanism of oxidation of dihydroorotate to orotate catalysed by human class 2 dihydroorotate dehydrogenase: a QM/MM free energy study. Phys Chem Chem Phys 2015; 17:17790-6. [PMID: 26087682 DOI: 10.1039/c5cp02016f] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The dihydroorotate dehydrogenase (DHOD) enzyme catalyzes the unique redox reaction in the de novo pyrimidine biosynthesis pathway. In this reaction, the oxidation of dihydroorotate (DHO) to orotate (OA) and reduction of the flavin mononucleotide (FMN) cofactor is catalysed by DHOD. The class 2 DHOD, to which the human enzyme belongs, was experimentally shown to follow a stepwise mechanism but the data did not allow the determination of the order of bond-breaking in a stepwise oxidation of DHO. The goal of this study is to understand the reaction mechanism at the molecular level of class 2 DHOD, which may aid in the design of inhibitors that selectively impact the activity of only certain members of the enzyme family. In this paper, the catalytic mechanism of oxidation of DHO to OA in human DHOD was studied using a hybrid Quantum Mechanical/Molecular Mechanical (QM/MM) approach and Molecular Dynamics (MD) simulations. The free energy barriers calculated reveal that the mechanism in human DHOD occurs via a stepwise reaction pathway. In the first step, a proton is abstracted from the C5 of DHO to the deprotonated Ser215 side chain. Whereas, in the second step, the transfer of the hydride or hydride equivalent from the C6 of DHO to the N5 of FMN, where free energy barrier calculated by the DFT/MM level is 10.84 kcal mol(-1). Finally, a residual decomposition analysis was carried out in order to elucidate the influence of the catalytic region residues during DHO oxidation.
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Affiliation(s)
- Cláudio Nahum Alves
- Laboratório de Planejamento e Desenvolvimento de Fármacos, Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, Belém, Brazil. mail:
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27
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Pharmacophore modeling for anti-Chagas drug design using the fragment molecular orbital method. PLoS One 2015; 10:e0125829. [PMID: 25961853 PMCID: PMC4427443 DOI: 10.1371/journal.pone.0125829] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2014] [Accepted: 03/26/2015] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Chagas disease, caused by the parasite Trypanosoma cruzi, is a neglected tropical disease that causes severe human health problems. To develop a new chemotherapeutic agent for the treatment of Chagas disease, we predicted a pharmacophore model for T. cruzi dihydroorotate dehydrogenase (TcDHODH) by fragment molecular orbital (FMO) calculation for orotate, oxonate, and 43 orotate derivatives. METHODOLOGY/PRINCIPAL FINDINGS Intermolecular interactions in the complexes of TcDHODH with orotate, oxonate, and 43 orotate derivatives were analyzed by FMO calculation at the MP2/6-31G level. The results indicated that the orotate moiety, which is the base fragment of these compounds, interacts with the Lys43, Asn67, and Asn194 residues of TcDHODH and the cofactor flavin mononucleotide (FMN), whereas functional groups introduced at the orotate 5-position strongly interact with the Lys214 residue. CONCLUSIONS/SIGNIFICANCE FMO-based interaction energy analyses revealed a pharmacophore model for TcDHODH inhibitor. Hydrogen bond acceptor pharmacophores correspond to Lys43 and Lys214, hydrogen bond donor and acceptor pharmacophores correspond to Asn67 and Asn194, and the aromatic ring pharmacophore corresponds to FMN, which shows important characteristics of compounds that inhibit TcDHODH. In addition, the Lys214 residue is not conserved between TcDHODH and human DHODH. Our analysis suggests that these orotate derivatives should preferentially bind to TcDHODH, increasing their selectivity. Our results obtained by pharmacophore modeling provides insight into the structural requirements for the design of TcDHODH inhibitors and their development as new anti-Chagas drugs.
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28
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Reis RAG, Lorenzato E, Silva VC, Nonato MC. Recombinant production, crystallization and crystal structure determination of dihydroorotate dehydrogenase from Leishmania (Viannia) braziliensis. ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS 2015; 71:547-52. [PMID: 25945707 DOI: 10.1107/s2053230x15000886] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2014] [Accepted: 01/15/2015] [Indexed: 11/11/2022]
Abstract
The enzyme dihydroorotate dehydrogenase (DHODH) is a flavoenzyme that catalyses the oxidation of dihydroorotate to orotate in the de novo pyrimidine-biosynthesis pathway. In this study, a reproducible protocol for the heterologous expression of active dihydroorotate dehydrogenase from Leishmania (Viannia) braziliensis (LbDHODH) was developed and its crystal structure was determined at 2.12 Å resolution. L. (V.) braziliensis is the species responsible for the mucosal form of leishmaniasis, a neglected disease for which no cure or effective therapy is available. Analyses of sequence, structural and kinetic features classify LbDHODH as a member of the class 1A DHODHs and reveal a very high degree of structural conservation with the previously reported structures of orthologous trypanosomatid enzymes. The relevance of nucleotide-biosynthetic pathways for cell metabolism together with structural and functional differences from the respective host enzyme suggests that inhibition of LbDHODH could be exploited for antileishmanicidal drug development. The present work provides the framework for further integrated in vitro, in silico and in vivo studies as a new tool to evaluate DHODH as a drug target against trypanosomatid-related diseases.
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Affiliation(s)
- Renata Almeida Garcia Reis
- Departamento de Física e Química, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Avenida Café S/N, 14040-903 Ribeirão Preto-SP, Brazil
| | - Eder Lorenzato
- Departamento de Física e Química, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Avenida Café S/N, 14040-903 Ribeirão Preto-SP, Brazil
| | - Valeria Cristina Silva
- Departamento de Física e Química, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Avenida Café S/N, 14040-903 Ribeirão Preto-SP, Brazil
| | - Maria Cristina Nonato
- Departamento de Física e Química, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Avenida Café S/N, 14040-903 Ribeirão Preto-SP, Brazil
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Silva JRA, Roitberg AE, Alves CN. A QM/MM free energy study of the oxidation mechanism of dihydroorotate dehydrogenase (class 1A) from Lactococcus lactis. J Phys Chem B 2015; 119:1468-73. [PMID: 25564307 DOI: 10.1021/jp512860r] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The dihydroorotate dehydrogenase (DHOD) class 1A enzyme catalyzes is the only redox enzyme in the biosynthetic pathway (de novo) of pyrimidines where dihydroorotate (DHO) is oxidized to orotate (OA) coupled to reduction of a flavin mononucleotide (FMN) cofactor. The rupture of two DHO C-H bonds can proceed in a concerted or stepwise way. Herein, the catalytic mechanism of DHOD from Lactococcus lactis involving DHO oxidation (first half-reaction) was described using a hybrid quantum mechanics/molecular mechanics (QM/MM) approach and molecular dynamics simulations. The free energy profile obtained from self-consistent charge-density functional tight binding/molecular mechanics calculations (corrected by DFT/MM) reveals that this occurs with the proton abstraction from DHO C5 to Cys130 deprotonated and DHO H6 is transferred to FMN N5 in a concerted mechanism with a very low barrier of 5.64 kcal/mol. Finally, through a residual decomposition analysis, the residues that have the main influence on the redox reaction were identified.
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Affiliation(s)
- José Rogério A Silva
- Laboratório de Planejamento e Desenvolvimento de Fármacos, Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará , Belém, PA 66075-110, Brazil
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30
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Munier-Lehmann H, Vidalain PO, Tangy F, Janin YL. On dihydroorotate dehydrogenases and their inhibitors and uses. J Med Chem 2013; 56:3148-67. [PMID: 23452331 DOI: 10.1021/jm301848w] [Citation(s) in RCA: 151] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Proper nucleosides availability is crucial for the proliferation of living entities (eukaryotic cells, parasites, bacteria, and virus). Accordingly, the uses of inhibitors of the de novo nucleosides biosynthetic pathways have been investigated in the past. In the following we have focused on dihydroorotate dehydrogenase (DHODH), the fourth enzyme in the de novo pyrimidine nucleosides biosynthetic pathway. We first described the different types of enzyme in terms of sequence, structure, and biochemistry, including the reported bioassays. In a second part, the series of inhibitors of this enzyme along with a description of their potential or actual uses were reviewed. These inhibitors are indeed used in medicine to treat autoimmune diseases such as rheumatoid arthritis or multiple sclerosis (leflunomide and teriflunomide) and have been investigated in treatments of cancer, virus, and parasite infections (i.e., malaria) as well as in crop science.
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Affiliation(s)
- Hélène Munier-Lehmann
- Institut Pasteur, Unité de Chimie et Biocatalyse, Département de Biologie Structurale et Chimie, 28 Rue du Dr. Roux, 75724 Paris Cedex 15, France
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31
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Harada S, Inaoka DK, Ohmori J, Kita K. Diversity of parasite complex II. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2013; 1827:658-67. [PMID: 23333273 DOI: 10.1016/j.bbabio.2013.01.005] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2012] [Revised: 01/07/2013] [Accepted: 01/09/2013] [Indexed: 10/27/2022]
Abstract
Parasites have developed a variety of physiological functions necessary for completing at least part of their life cycles in the specialized environments of surrounding the parasites in the host. Regarding energy metabolism, which is essential for survival, parasites adapt to the low oxygen environment in mammalian hosts by using metabolic systems that are very different from those of the hosts. In many cases, the parasite employs aerobic metabolism during the free-living stage outside the host but undergoes major changes in developmental control and environmental adaptation to switch to anaerobic energy metabolism. Parasite mitochondria play diverse roles in their energy metabolism, and in recent studies of the parasitic nematode, Ascaris suum, the mitochondrial complex II plays an important role in anaerobic energy metabolism of parasites inhabiting hosts by acting as a quinol-fumarate reductase. In Trypanosomes, parasite complex II has been found to have a novel function and structure. Complex II of Trypanosoma cruzi is an unusual supramolecular complex with a heterodimeric iron-sulfur subunit and seven additional non-catalytic subunits. The enzyme shows reduced binding affinities for both substrates and inhibitors. Interestingly, this structural organization is conserved in all trypanosomatids. Since the properties of complex II differ across a wide range of parasites, this complex is a potential target for the development of new chemotherapeutic agents. In this regard, structural information on the target enzyme is essential for the molecular design of drugs. This article is part of a Special Issue entitled: Respiratory complex II: Role in cellular physiology and disease.
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Affiliation(s)
- Shigeharu Harada
- Department of Applied Biology, Kyoto Institute of Technology, Kyoto, Japan.
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32
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de Farias Silva N, Lameira J, Alves CN, Martí S. Computational study of the mechanism of half-reactions in class 1A dihydroorotate dehydrogenase from Trypanosoma cruzi. Phys Chem Chem Phys 2013; 15:18863-71. [DOI: 10.1039/c3cp52692e] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Cordeiro AT, Feliciano PR, Pinheiro MP, Nonato MC. Crystal structure of dihydroorotate dehydrogenase from Leishmania major. Biochimie 2012; 94:1739-48. [DOI: 10.1016/j.biochi.2012.04.003] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2012] [Accepted: 04/03/2012] [Indexed: 01/09/2023]
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34
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Shimizu H, Osanai A, Sakamoto K, Inaoka DK, Shiba T, Harada S, Kita K. Crystal structure of mitochondrial quinol-fumarate reductase from the parasitic nematode Ascaris suum. J Biochem 2012; 151:589-92. [DOI: 10.1093/jb/mvs051] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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Couto SG, Cristina Nonato M, Costa-Filho AJ. Site directed spin labeling studies of Escherichia coli dihydroorotate dehydrogenase N-terminal extension. Biochem Biophys Res Commun 2011; 414:487-92. [PMID: 21986535 DOI: 10.1016/j.bbrc.2011.09.092] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2011] [Accepted: 09/19/2011] [Indexed: 11/29/2022]
Abstract
Dihydroorotate dehydrogenases (DHODHs) are enzymes that catalyze the fourth step of the de novo synthesis of pyrimidine nucleotides. In this reaction, DHODH converts dihydroorotate to orotate, using a flavine mononucleotide as a cofactor. Since the synthesis of nucleotides has different pathways in mammals as compared to parasites, DHODH has gained much attention as a promising target for drug design. Escherichia coli DHODH (EcDHODH) is a family 2 DHODH that interacts with cell membranes in order to promote catalysis. The membrane association is supposedly made via an extension found in the enzyme's N-terminal. In the present work, we used site directed spin labeling (SDSL) to specifically place a magnetic probe at positions 2, 5, 19, and 21 within the N-terminal and thus monitor, by using Electron Spin Resonance (ESR), dynamics and structural changes in this region in the presence of a membrane model system. Overall, our ESR spectra show that the N-terminal indeed binds to membranes and that it experiences a somewhat high flexibility that could be related to the role of this region as a molecular lid controlling the entrance of the enzyme's active site and thus allowing the enzyme to give access to quinones that are dispersed in the membrane and that are necessary for the catalysis.
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Affiliation(s)
- Sheila G Couto
- Instituto de Física de São Carlos, Universidade de São Paulo, Av. Trabalhador São-carlense 400, C.P. 369, 13560-970, São Carlos, SP, Brazil
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Novel insights for dihydroorotate dehydrogenase class 1A inhibitors discovery. Eur J Med Chem 2010; 45:5899-909. [DOI: 10.1016/j.ejmech.2010.09.055] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2010] [Revised: 09/21/2010] [Accepted: 09/23/2010] [Indexed: 11/22/2022]
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37
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Kinetic mechanism and catalysis of Trypanosoma cruzi dihydroorotate dehydrogenase enzyme evaluated by isothermal titration calorimetry. Anal Biochem 2010; 399:13-22. [DOI: 10.1016/j.ab.2009.11.018] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2009] [Revised: 11/14/2009] [Accepted: 11/15/2009] [Indexed: 11/20/2022]
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38
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Fagan RL, Palfey BA. Roles in binding and chemistry for conserved active site residues in the class 2 dihydroorotate dehydrogenase from Escherichia coli. Biochemistry 2009; 48:7169-78. [PMID: 19530672 DOI: 10.1021/bi900370s] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Dihydroorotate dehydrogenases (DHODs) catalyze the only redox step in de novo pyrimidine biosynthesis, the oxidation of dihydroorotate (DHO) to orotate (OA). During the reaction, the hydrogen at C6 of DHO is transferred to N5 of the isoalloxazine ring of an enzyme-bound FMN prosthetic group as a hydride, and an active site base (Ser175 in the class 2 DHOD from Escherichia coli) deprotonates C5 of DHO. Aside from the identity of the active site base, the pyrimidine binding site of all DHODs is nearly identical. Several strictly conserved residues (four asparagines and either a serine or threonine) make extensive hydrogen bonds to the pyrimidine). The roles these conserved residues play in DHO oxidation are unknown. Site-directed mutagenesis was used to investigate the role of each residue during DHO oxidation. The effects of each mutation on substrate and product binding, as well as the effect on the rate constant of the chemical step, were determined. The effects of the mutations ranged from negligible to severe. Some of the residues were very important for chemistry, while others were important for binding. Mutation of residues capable of stabilizing reaction intermediates resulted in large decreases in the rate constant of the chemical step, suggesting these residues are quite important for stabilizing charge buildup in the active site. This finding is consistent with previous results that class 2 DHODs use a stepwise mechanism for DHO oxidation.
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Affiliation(s)
- Rebecca L Fagan
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, Michigan 48109-5606, USA
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Kow RL, Whicher JR, McDonald CA, Palfey BA, Fagan RL. Disruption of the proton relay network in the class 2 dihydroorotate dehydrogenase from Escherichia coli. Biochemistry 2009; 48:9801-9. [PMID: 19694481 DOI: 10.1021/bi901024m] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Dihydroorotate dehydrogenases (DHODs) are FMN-containing enzymes that catalyze the conversion of dihydroorotate (DHO) to orotate in the de novo synthesis of pyrimidines. During the reaction, a proton is transferred from C5 of DHO to an active site base and the hydrogen at C6 of DHO is transferred to N5 of the isoalloxazine ring of the flavin as a hydride. In class 2 DHODs, a hydrogen bond network observed in crystal structures has been proposed to deprotonate the C5 atom of DHO. The active site base (Ser175 in the Escherichia coli enzyme) hydrogen bonds to a crystallographic water molecule that sits on a phenylalanine (Phe115 in the E. coli enzyme) and hydrogen bonds to a threonine (Thr178 in the E. coli enzyme), residues that are conserved in class 2 enzymes. The importance of these residues in the oxidation of DHO was investigated using site-directed mutagenesis. Mutating Ser175 to alanine had severe effects on the rate of flavin reduction, slowing it by more than 3 orders of magnitude. Changing the size and/or hydrophobicity of the residues of the hydrogen bond network, Thr178 and Phe115, slowed flavin reduction as much as 2 orders of magnitude, indicating that the active site base and the hydrogen bond network work together for efficient deprotonation of DHO.
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Affiliation(s)
- Rebecca L Kow
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, Michigan 48109-5606, USA
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40
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Osanai A, Harada S, Sakamoto K, Shimizu H, Inaoka DK, Kita K. Crystallization of mitochondrial rhodoquinol-fumarate reductase from the parasitic nematode Ascaris suum with the specific inhibitor flutolanil. Acta Crystallogr Sect F Struct Biol Cryst Commun 2009; 65:941-4. [PMID: 19724139 PMCID: PMC2795607 DOI: 10.1107/s1744309109031352] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2009] [Accepted: 08/08/2009] [Indexed: 11/10/2022]
Abstract
In adult Ascaris suum (roundworm) mitochondrial membrane-bound complex II acts as a rhodoquinol-fumarate reductase, which is the reverse reaction to that of mammalian complex II (succinate-ubiquinone reductase). The adult A. suum rhodoquinol-fumarate reductase was crystallized in the presence of octaethyleneglycol monododecyl ether and n-dodecyl-beta-D-maltopyranoside in a 3:2 weight ratio. The crystals belonged to the orthorhombic space group P2(1)2(1)2(1), with unit-cell parameters a = 123.75, b = 129.08, c = 221.12 A, and diffracted to 2.8 A resolution using synchrotron radiation. The presence of two molecules in the asymmetric unit (120 kDa x 2) gives a crystal volume per protein mass (V(M)) of 3.6 A(3) Da(-1).
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Affiliation(s)
- Arihiro Osanai
- Department of Biomedical Chemistry, Graduate School of Medicine, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Shigeharu Harada
- Department of Applied Biology, Graduate School of Science and Technology, Kyoto Institute of Technology, Sakyo-ku, Kyoto 606-8585, Japan
| | - Kimitoshi Sakamoto
- Department of Biomedical Chemistry, Graduate School of Medicine, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Hironari Shimizu
- Department of Biomedical Chemistry, Graduate School of Medicine, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Daniel Ken Inaoka
- Department of Biomedical Chemistry, Graduate School of Medicine, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Kiyoshi Kita
- Department of Biomedical Chemistry, Graduate School of Medicine, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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